Blog Archives

High Resolution Figures in R

March 12, 2013
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High Resolution Figures in R

As I was recently preparing a manuscript for PLOS ONE, I realized the default resolution of R and RStudio images are insufficient for publication. PLOS ONE requires 300 ppi images in TIFF or EPS (encapsulated postscript) format. In R plots … Continue reading →

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No Statistical Panacea, Hierarchical or Otherwise

February 13, 2013
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No Statistical Panacea, Hierarchical or Otherwise

Everyone in academia knows how painful the peer-review publication process can be. It’s a lot like Democracy, in that it’s the worst system ever invented, except for all the others. The peer-review process does a fair job at promoting good … Continue reading →

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Effects of forest management on a woodland salamander in Missouri

January 25, 2013
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Effects of forest management on a woodland salamander in Missouri

Effects of experimental forest management on a terrestrial, woodland salamander in Missouri by Daniel J. Hocking, Grant M. Connette, Christopher A. Conner, Brett R. Scheffers, Shannon E. Pittman, William E. Peterman, and Raymond D. Semlitsch. This is the first post … Continue reading →

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Building R packages: missing path to pdflatex

December 15, 2012
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Building R packages: missing path to pdflatex

Recently whiling trying to build an R package for generalized estimating equation model selection (QICpack on github), I was getting an error related to latex creating the PDF package manuals. It seems like this is a relatively common problem on … Continue reading →

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GEE QIC update

November 15, 2012
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GEE QIC update

Here is improved code for calculating QIC from geeglm in geepack in R (original post). Let me know how it works. I haven’t tested it much, but is seems that QIC may select overparameterized models. In the code below, I … Continue reading →

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Stan for Bayesian Analysis

October 23, 2012
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Stan for Bayesian Analysis

Bayesian analysis has been growing in popularity among ecologists recently, largely due to accessible books such as Models for Ecological Data: An Introduction, Introduction to WinBUGS for Ecologists, and Bayesian Methods for Ecology. Most ecologists with limited programming background have … Continue reading →

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Plotting 95% Confidence Bands in R

July 26, 2012
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Plotting 95% Confidence Bands in R

I am comparing estimates from subject-specific GLMMs and population-average GEE models as part of a publication I am working on. As part of this, I want to visualize predictions of each type of model including 95% confidence bands. First I had to ma...

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Installing and Running JAGS on Mac OS 10.5.8

March 26, 2012
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Installing and Running JAGS on Mac OS 10.5.8

JAGS is an alternative to BUGS (WinBUGS or OpenBUGS) for conducting a Bayesian Analysis. It stands for Just Another Gibbs Sampler, and like WinBUGS, it is essentially an MCMC machine that employs a Gibbs sampler so you don't have to write your own for ...

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R script to calculate QIC for Generalized Estimating Equation (GEE) Model Selection

March 23, 2012
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R script to calculate QIC for Generalized Estimating Equation (GEE) Model Selection

Generalized Estimating Equations (GEE) can be used to analyze longitudinal count data; that is, repeated counts taken from the same subject or site. This is often referred to as repeated measures data, but longitudinal data often has more repeated obse...

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Plotting grouped data vs time with error bars in R

October 31, 2011
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Plotting grouped data vs time with error bars in R

This is my first blog since joiningR-bloggers. I’m quite excited to be part of this group and apologize if I boreany experienced R users with my basic blogs for learning R or offendprogrammers with my inefficient, sloppy coding. Hopefully writing for...

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